SWISS-PROT and 2D gel databases
Two-dimensional (2D) gel techniques have made enormous progress in the last
few years. One of the consequences of this evolution has been the development
of databases that contain master gels from a variety of mammalian tissues or
from bacterial sources. These databases are going to play an increasingly
important role in the analysis of genomes and of molecular diseases. 2D gel
databases generally contain one or more master images of the gels that
correspond to the tissue or organism studied; spots on these images are
attributed an identification code and a variable percentage of these spots
are linked to known proteins. The identification of a protein on a 2D gel is
generally carried out using antibodies or by microsequencing. Microsequencing
of 2D gel spots also produces partial sequences and physico-chemical data for
a number of yet uncharacterized proteins.
SWISS-PROT has committed itself to work in close collaboration with a number
of groups developing 2D gel databases. Since last year cross-references are
already available to the gene-protein database of Escherichia coli K-12 (now
called ECO2DBASE) [1] and symmetrically that database now contains cross-
references to SWISS-PROT. As a second step we have expanded our links to
2D gel databases by integrating data from the following sources:
- The Human 2D gel protein database of the Faculty of Medicine of the
University of Geneva (known as SWISS-2DPAGE). SWISS-2DPAGE currently
contains data concerning plasma [2] and liver [3] proteins, but will
soon include additional tissues.
- The Human keratinocyte 2D gel protein database from the universities
of Aarhus and Ghent [4] (known as AARHUS/GHENT-2DPAGE).
For both of these databases we provide:
a) Cross-references (using the DR line) to the identificators for the spots
corresponding to known or unknown microsequenced proteins.
b) We have created new entries for microsequences that correspond to novel,
yet unidentified, proteins [see the example in the appendix].
c) In some cases we have entered the extent of the microsequences for
already known proteins. This was done for proteins which are not yet
well characterized. The availability of such microsequences allows, for
example, to confirm the position of a signal sequence cleavage site or
to confirm the correctness of a translated genomic sequence.
In the near future the collaboration with the group of D. Hochstrasser which
produces the SWISS-2DPAGE database will be expanded in the following
directions:
a) The MELANIE software package [5] which is a complete system for the
analysis of 2D gels and which is developed by the group of Hochstrasser
will allow its users to navigate back and forth between SWISS-2DPAGE and
SWISS-PROT.
For more information on Melanie, please contact Dr. Ron Appel:
Email: appel at cih.hcuge.ch
Tel: +41-22-372 62 64
Fax: +41-22-372 61 98
b) A file server will be set up that will allow anyone with a network
connection to obtain annotated graphic files containing the region of
the gels that correspond to a selected SWISS-PROT entry linked to SWISS-
2DPAGE.
[1] VanBogelen R.A., Sankar P., Clark R.L., Bogan J.A., Neidhardt F.C.
Electrophoresis 13:1014-1054(1992).
[2] Hughes G.J., Frutiger S., Paquet N., Ravier F., Pasquali C.,
Sanchez J.-C., James R., Tissot J.-D., Bjellqvist B.,Hochstrasser D.F.
Electrophoresis 13:707-714(1992).
[3] Hochstrasser D.F., Frutiger S., Paquet N., Bairoch A., Ravier F.,
Pasquali C., Sanchez J.-C., Tissot J.-D., Bjellqvist B., Vargas R.,
Appel R.D., Hughes G.J.
Electrophoresis 13:992-1001(1992).
[4] Celis J.E., Rasmussen H.H., Madsen P., Leffers H., Honore B., Dejgaard K.,
Gesser B., Olsen E., Gromov P., Hoffmann H.J., Nielsen M., Celis A.,
Basse B., Lauridsen J.B., Ratz G.P., Nielsen H., Andersen A.H., Walbum E.,
Kjaergaard I., Puype M., Van Damme J., Vandekerckhove J.
Electrophoresis 13:893-959(1992).
[5] Appel R., Hochstrasser D.F., Funk M., Vargas J.R., Pellegrini C.,
Muller A.F., Scherrer J.-R.
Electrophoresis 12:722-735(1991).
Appendix: example of a newly entered SWISS-PROT entry corresponding to a
unknown liver protein in SWISS-2DPAGE.
ID ULA1_HUMAN STANDARD; PRT; 10 AA.
AC P30036;
DT 01-APR-1993 (REL. 25, CREATED)
DT 01-APR-1993 (REL. 25, LAST SEQUENCE UPDATE)
DT 01-APR-1993 (REL. 25, LAST ANNOTATION UPDATE)
DE UNKNOWN PROTEIN FROM 2D-PAGE OF LIVER TISSUE (SPOT 2) (FRAGMENT).
OS HOMO SAPIENS (HUMAN).
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA;
OC EUTHERIA; PRIMATES.
RN [1]
RP SEQUENCE.
RC TISSUE=LIVER;
RA HOCHSTRASSER D.F., FRUTIGER S., PAQUET N., BAIROCH A., RAVIER F.,
RA PASQUALI C., SANCHEZ J.-C., TISSOT J.-D., BJELLQVIST B., VARGAS R.,
RA APPEL R.D., HUGHES G.J.;
RL ELECTROPHORESIS 13:992-1001(1992).
CC -!- ON THE 2D-GEL THE DETERMINED PI OF THIS UNKNOWN PROTEIN IS: 5.45,
CC ITS MW IS: 70 KD.
DR SWISS-2DPAGE; P30036; HUMAN.
FT NON_TER 1 1
FT NON_TER 10 10
SQ SEQUENCE 10 AA; 965 MW; 515 CN;
ASEAHXGAVN
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